{"id":"https://openalex.org/W1482582909","doi":"https://doi.org/10.1089/153623103322006661","title":"A Life Scientist's Gateway to Distributed Data Management and Computing: The PathPort/ToolBus Framework","display_name":"A Life Scientist's Gateway to Distributed Data Management and Computing: The PathPort/ToolBus Framework","publication_year":2003,"publication_date":"2003-01-01","ids":{"openalex":"https://openalex.org/W1482582909","doi":"https://doi.org/10.1089/153623103322006661","mag":"1482582909","pmid":"https://pubmed.ncbi.nlm.nih.gov/12831562"},"language":"en","primary_location":{"id":"doi:10.1089/153623103322006661","is_oa":false,"landing_page_url":"https://doi.org/10.1089/153623103322006661","pdf_url":null,"source":{"id":"https://openalex.org/S116972989","display_name":"OMICS A Journal of Integrative Biology","issn_l":"1536-2310","issn":["1536-2310","1557-8100"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"OMICS: A Journal of Integrative Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070316700","display_name":"J. Dana Eckart","orcid":null},"institutions":[{"id":"https://openalex.org/I859038795","display_name":"Virginia Tech","ror":"https://ror.org/02smfhw86","country_code":"US","type":"education","lineage":["https://openalex.org/I859038795"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J. Dana Eckart","raw_affiliation_strings":["Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia","Virginia Bioinformatics Institute , Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, Virginia","institution_ids":["https://openalex.org/I859038795"]},{"raw_affiliation_string":"Virginia Bioinformatics Institute , Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, USA","institution_ids":["https://openalex.org/I859038795"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058609337","display_name":"Bruno Sobral","orcid":"https://orcid.org/0000-0003-3908-577X"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bruno W. S. Sobral","raw_affiliation_strings":[""],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":13.5847,"has_fulltext":false,"cited_by_count":41,"citation_normalized_percentile":{"value":0.98484848,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"7","issue":"1","first_page":"79","last_page":"88"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.995199978351593,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.995199978351593,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9914000034332275,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9837999939918518,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/interoperability","display_name":"Interoperability","score":0.7827014327049255},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6923889517784119},{"id":"https://openalex.org/keywords/standardization","display_name":"Standardization","score":0.5973707437515259},{"id":"https://openalex.org/keywords/data-management","display_name":"Data management","score":0.5607154369354248},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.5468962788581848},{"id":"https://openalex.org/keywords/gateway","display_name":"Gateway (web page)","score":0.511403501033783},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.5032822489738464},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.4818647801876068},{"id":"https://openalex.org/keywords/web-service","display_name":"Web service","score":0.4590631127357483},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.45716559886932373},{"id":"https://openalex.org/keywords/pace","display_name":"Pace","score":0.4224429726600647},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.41594916582107544},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.293207585811615}],"concepts":[{"id":"https://openalex.org/C20136886","wikidata":"https://www.wikidata.org/wiki/Q749647","display_name":"Interoperability","level":2,"score":0.7827014327049255},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6923889517784119},{"id":"https://openalex.org/C188087704","wikidata":"https://www.wikidata.org/wiki/Q369577","display_name":"Standardization","level":2,"score":0.5973707437515259},{"id":"https://openalex.org/C1668388","wikidata":"https://www.wikidata.org/wiki/Q1149776","display_name":"Data management","level":2,"score":0.5607154369354248},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.5468962788581848},{"id":"https://openalex.org/C2777710495","wikidata":"https://www.wikidata.org/wiki/Q5527195","display_name":"Gateway (web page)","level":2,"score":0.511403501033783},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.5032822489738464},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4818647801876068},{"id":"https://openalex.org/C35578498","wikidata":"https://www.wikidata.org/wiki/Q193424","display_name":"Web service","level":2,"score":0.4590631127357483},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.45716559886932373},{"id":"https://openalex.org/C2777526511","wikidata":"https://www.wikidata.org/wiki/Q691543","display_name":"Pace","level":2,"score":0.4224429726600647},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.41594916582107544},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.293207585811615},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D001690","descriptor_name":"Biological Science Disciplines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001690","descriptor_name":"Biological Science Disciplines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001690","descriptor_name":"Biological Science Disciplines","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018511","descriptor_name":"Systems Integration","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1089/153623103322006661","is_oa":false,"landing_page_url":"https://doi.org/10.1089/153623103322006661","pdf_url":null,"source":{"id":"https://openalex.org/S116972989","display_name":"OMICS A Journal of Integrative Biology","issn_l":"1536-2310","issn":["1536-2310","1557-8100"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"OMICS: A Journal of Integrative Biology","raw_type":"journal-article"},{"id":"pmid:12831562","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12831562","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Omics : a journal of integrative biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W40003979","https://openalex.org/W1239375374","https://openalex.org/W1519646691","https://openalex.org/W1597538863","https://openalex.org/W1608152890","https://openalex.org/W1649645444","https://openalex.org/W1992178984","https://openalex.org/W2124165983","https://openalex.org/W2124464500","https://openalex.org/W2134062730","https://openalex.org/W2166699767","https://openalex.org/W2169929748","https://openalex.org/W2172143128","https://openalex.org/W2465815624","https://openalex.org/W4246066782","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2386723501","https://openalex.org/W2387879414","https://openalex.org/W2390304029","https://openalex.org/W2354923724","https://openalex.org/W2093262417","https://openalex.org/W2146830340","https://openalex.org/W4288601434","https://openalex.org/W2377101853","https://openalex.org/W2362180844","https://openalex.org/W2123131699"],"abstract_inverted_index":{"The":[0,11,131],"emergent":[1],"needs":[2],"of":[3,13,63,67,123,135],"the":[4,28,39,64,124,128,164,170],"bioinformatics":[5,129],"community":[6],"challenge":[7],"current":[8],"information":[9],"systems.":[10],"pace":[12],"biological":[14,32],"data":[15,36,46,55,92,96,102,141,184],"generation":[16,57],"far":[17],"outstrips":[18],"Moore's":[19],"Law.":[20],"Therefore,":[21],"a":[22,49,114,136,156,172,179,191],"gap":[23],"continues":[24],"to":[25,30,41,74,89,119,139,150],"widen":[26],"between":[27],"capabilities":[29,66],"produce":[31],"(molecular":[33],"and":[34,38,43,70,77,97,101,105,143,185,187],"cell)":[35],"sets":[37],"capability":[40],"manage":[42],"analyze":[44],"these":[45],"sets.":[47],"As":[48],"result,":[50],"Federal":[51],"investments":[52],"in":[53,61,155],"large":[54],"set":[56],"produces":[58],"diminishing":[59],"returns":[60],"terms":[62],"community's":[65],"understanding":[68,73],"biology":[69],"leveraging":[71],"that":[72,80],"make":[75],"scientific":[76],"technological":[78],"advances":[79],"improve":[81],"society.":[82],"We":[83],"are":[84],"building":[85],"an":[86],"open":[87],"framework":[88,118,158],"address":[90],"various":[91],"management":[93,142],"issues":[94],"including":[95],"tool":[98],"interoperability,":[99],"nomenclature":[100],"communication":[103],"standardization,":[104],"database":[106],"integration.":[107],"PathPort,":[108],"short":[109],"for":[110,145,182],"Pathogen":[111],"Portal,":[112],"employs":[113],"generic,":[115],"web-services":[116],"based":[117],"deal":[120],"with":[121],"some":[122],"problems":[125],"identified":[126],"by":[127],"community.":[130],"motivating":[132],"research":[133],"goal":[134],"scalable":[137],"system":[138],"provide":[140],"analysis":[144],"key":[146],"pathosystems,":[147],"especially":[148],"relating":[149],"molecular":[151],"data,":[152],"has":[153],"resulted":[154],"generic":[157],"using":[159],"two":[160],"major":[161],"components.":[162],"On":[163,169],"server-side,":[165],"we":[166],"employ":[167],"web-services.":[168],"client-side,":[171],"Java":[173],"application":[174],"called":[175],"ToolBus":[176],"acts":[177],"as":[178],"client-side":[180],"\"bus\"":[181],"contacting":[183],"tools":[186],"viewing":[188],"results":[189],"through":[190],"single,":[192],"consistent":[193],"user":[194],"interface.":[195]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
